What file formats are returned for compound structures?

The skill can retrieve molecular structures in MOL file format for chemical informatics or PNG format for visual identification.

Can I filter studies by specific diseases or species?

Yes, you can use the MetStat context to filter studies by analytical platform (LCMS/GCMS), species (Human/Mouse), sample source, and specific conditions like Diabetes or Cancer.

Does it support nomenclature standardization?

Yes, it utilizes the RefMet database to match common metabolite names to standardized systematic names and hierarchical classifications (super class, main class, etc.).

Can I use this for mass spectrometry identification?

Yes, the skill supports searching by mass-to-charge ratio (m/z) with specific ion adducts and tolerance levels to identify potential compounds across multiple databases.

What data can I access with this skill?

You can access over 4,200 processed metabolomics studies, metabolite structures, experimental metadata, and nomenclature standards from the NIH Metabolomics Workbench repository.

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: pur3v4d3r

bypur3v4d3r

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Data Science & ML

Accesses and queries the NIH Metabolomics Workbench repository for metabolite structures, experimental study data, and standardized nomenclature.

This skill provides programmatic access to the NIH Common Fund-sponsored Metabolomics Workbench, a premier repository for metabolomics research data. It enables researchers and developers to query over 4,200 studies, perform mass spectrometry searches by m/z ratio, and standardize metabolite nomenclature using the RefMet database. Whether you are performing biomarker discovery, cross-referencing compound identifiers (PubChem, KEGG, HMDB), or retrieving gene-metabolite associations, this skill streamlines the integration of large-scale metabolomics datasets into your Claude Code workflows.

Key Features

01Standardized metabolite nomenclature and classification via RefMet

021 GitHub stars

03Retrieval of metabolite structures (MOL/PNG) and cross-database identifiers

04Access to 4,200+ processed metabolomics studies and experimental metadata

05Mass spectrometry searches by m/z ratio and ion adducts

06Querying of gene and protein associations for metabolic pathways

Use Cases

01Identifying unknown compounds from mass spectrometry (m/z) peak lists

02Automating the retrieval of experimental datasets for biomarker discovery projects

03Standardizing metabolite naming conventions across diverse scientific datasets

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add pur3v4d3r/pur3-pkb-codebase metabolomics-workbench-database

For use in Claude.ai and ChatGPT

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